Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.
☆162Sep 18, 2026Updated 3 weeks ago
Alternatives and similar repositories for novae
Users that are interested in novae are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆295Sep 15, 2026Updated 3 weeks ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆193Sep 22, 2026Updated 2 weeks ago
- ☆142Feb 13, 2025Updated last year
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆99Jul 4, 2026Updated 3 months ago
- Single-cell spatial omics analysis that makes you happy!☆75Updated this week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- End-to-end analysis of spatial multi-omics data☆128Sep 20, 2026Updated 2 weeks ago
- A python package for Multiomics and Ecological Spatial Analysis (MESA)☆24Sep 30, 2026Updated last week
- Integrating histology and spatial transcriptomics - NeurIPS 2024☆442Apr 16, 2026Updated 5 months ago
- Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching, ICML2025 (Spotlight)☆38Aug 11, 2025Updated last year
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆89Nov 16, 2025Updated 10 months ago
- ☆22Jan 6, 2024Updated 2 years ago
- A Snakemake pipeline for Xenium data analysis.☆28Jul 22, 2026Updated 2 months ago
- Automatically annotate cell types, consistently across samples.☆30Updated this week
- Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effe…☆46Jul 8, 2026Updated 3 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Static plotting for spatialdata☆86Sep 28, 2026Updated last week
- Code for "SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics".☆55Sep 2, 2025Updated last year
- CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data☆34Jul 24, 2025Updated last year
- Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse☆71Updated this week
- R package for normalisation of spatial transcriptomics data☆20Sep 29, 2026Updated last week
- STPath: A Generative Foundation Model for Integrating Spatial Transcriptomics and Whole Slide Images☆53Jul 27, 2025Updated last year
- A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.☆39Updated this week
- Spatial alignment of single cell transcriptomic data.☆373Jul 1, 2025Updated last year
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆81Aug 22, 2026Updated last month
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Configure Vitessce using existing Scverse plotting APIs☆25Aug 7, 2026Updated 2 months ago
- An open and interoperable data framework for spatial omics data☆399Updated this week
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆197Updated this week
- Python API and Jupyter widget for Vitessce☆67Sep 22, 2026Updated 2 weeks ago
- CAST package☆43Oct 26, 2024Updated last year
- Spatial and multiomic visualization and analysis library☆65Updated this week
- Single-cell differential expression☆19Apr 23, 2026Updated 5 months ago
- Repository for Nicheformer: a foundation model for single-cell and spatial omics☆175Nov 23, 2025Updated 10 months ago
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆113Sep 28, 2026Updated last week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.☆17Updated this week
- A large scale benchmark for cross-modal learning of histology and spatial expressions☆24Oct 28, 2025Updated 11 months ago
- An offical repo for paper "Single-cells are Spatial Tokens: Transformers for Spatially Resolved Transcriptomics Data Imputation"☆18Aug 11, 2023Updated 3 years ago
- Pareto Task Inference in Python☆23Updated this week
- Profile purification of single-cell spatial transcriptomics data☆61Jun 29, 2026Updated 3 months ago
- Join subcellular Visium HD bins into cells☆144Sep 14, 2026Updated 3 weeks ago
- a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution☆56Aug 11, 2025Updated last year